ERDDAP > info > bcodmo_dataset_762511

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016.		I   M	background			BCO-DMO	bcodmo_dataset_762511

The Dataset's Variables and Attributes

Row Type	Variable Name	Attribute Name	Data Type	Value
attribute	NC_GLOBAL	access_formats	String	.htmlTable,.csv,.json,.mat,.nc,.tsv
attribute	NC_GLOBAL	acquisition_description	String	Colonies that displayed a strong bleaching phenotype in April 2015 were selected for transcriptome-wide gene expression analyses. These colonies were subsequently sampled in August 2015, December 2015 and April 2016. For these 36 field-collected tissue samples (five colonies of A. gemmifera and four colonies of A. hyacinthus across four sample dates), total RNA was extracted Qiagens RNAeasy Plus Kit. In total 36 cDNA libraries were generated using the Illumina TruSeq RNA Library Prep Kit v2 with Protoscript II Reverse Transcriptase. We carried out multiplexed Illumina sequencing at the University of Utah Microarray and Genomic Analysis Core Facility. Fastq files were mapped to a reference transcriptome (Barshis et al., 2013) using HISAT2 (Langmead & Salzberg, 2012) with a minimum mapping quality of 10. We used SAMtools (Li et al., 2009) to generate counts for each contig in our reference transcriptome. Counts matrices were normalized in DESeq2.0 (Love, Huber, & Anders, 2014). Approximate coordinates for this dataset are "Pool 400", back reef lagoon, Ofu, American Samoa (-14.17990, -169.65448)
attribute	NC_GLOBAL	awards_0_award_nid	String	647913
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1547921
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1547921
attribute	NC_GLOBAL	awards_0_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_0_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_0_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_0_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Sequence accessions: Hidden resilience to recurrent bleaching PI: Stephen Palumbi Data Version 1: 2019-03-18
attribute	NC_GLOBAL	Conventions	String	COARDS, CF-1.6, ACDD-1.3
attribute	NC_GLOBAL	creator_email	String	info at bco-dmo.org
attribute	NC_GLOBAL	creator_name	String	BCO-DMO
attribute	NC_GLOBAL	creator_type	String	institution
attribute	NC_GLOBAL	creator_url	String	https://www.bco-dmo.org/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	date_created	String	2019-03-18T18:45:27Z
attribute	NC_GLOBAL	date_modified	String	2019-04-26T21:24:46Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.762511.2
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/762511
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	762537
attribute	NC_GLOBAL	instruments_0_description	String	General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Automated DNA Sequencer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	649
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Illumina HiSeq 2500
attribute	NC_GLOBAL	keywords	String	accession, Accession_link, bco, bco-dmo, biological, bleaching, bleaching_status, chemical, colony, data, dataset, date, dmo, erddap, link, management, month, oceanography, office, preliminary, sample, species, status, year
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/762511/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/762511
attribute	NC_GLOBAL	param_mapping	String	{'762511': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/762511/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Stanford University
attribute	NC_GLOBAL	people_0_person_name	String	Stephen R. Palumbi
attribute	NC_GLOBAL	people_0_person_nid	String	51368
attribute	NC_GLOBAL	people_0_role	String	Principal Investigator
attribute	NC_GLOBAL	people_0_role_type	String	originator
attribute	NC_GLOBAL	people_1_affiliation	String	University of Western Australia
attribute	NC_GLOBAL	people_1_person_name	String	Luke Thomas
attribute	NC_GLOBAL	people_1_person_nid	String	762507
attribute	NC_GLOBAL	people_1_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_1_role_type	String	originator
attribute	NC_GLOBAL	people_2_affiliation	String	Stanford University
attribute	NC_GLOBAL	people_2_person_name	String	Stephen R. Palumbi
attribute	NC_GLOBAL	people_2_person_nid	String	51368
attribute	NC_GLOBAL	people_2_role	String	Contact
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	people_3_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_3_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_3_person_name	String	Amber York
attribute	NC_GLOBAL	people_3_person_nid	String	643627
attribute	NC_GLOBAL	people_3_role	String	Data Manager
attribute	NC_GLOBAL	people_3_role_type	String	related
attribute	NC_GLOBAL	project	String	Bleaching American Samoa
attribute	NC_GLOBAL	projects_0_acronym	String	Bleaching American Samoa
attribute	NC_GLOBAL	projects_0_description	String	Description from NSF award abstract: The strongest coral bleaching event in nearly 20 years began in American Samoa in January 2015. Coral bleaching occurs when ocean water temperatures exceed a coral's normal heat tolerance. But bleaching events usually show an unexplained pattern - colonies next to one another can show very different levels of bleaching - from pure white to the normal tan color of a healthy coral. The investigators have observed this pattern among 280 corals on reefs in American Samoa that have been studied for years. This system will be used to test four major hypotheses about what causes some corals to bleach and some not: differences in 1) species, 2) the temperature the corals experienced, 3) the symbiont they harbor, and 4) the genotype of the coral host. In addition, the investigators will return to American Samoa at regular intervals to measure the rate of recovery of each coral colony and conduct the same tests as above for recovery rate. The stark-white reefscapes left behind by bleaching events are one of the most common signals of increased ocean warming. This work will take advantage of years of prior study and the advent of a coral bleaching event to understand the rules for survival on reefs. The reefs of American Samoa began showing a major bleaching event starting in January 2015, including 62 corals that have been intensively studied for coral thermal resistance, field temperatures, and symbiont type. In April 2015 the investigators monitored bleaching status of these and additional corals, totaling 280 corals from four species, and uncovered marked variation in bleaching extent within and between species and within and between reef regions. The team will test the relative importance of microclimate to bleaching state by examining records of approximately 50 temperature loggers in place since before the bleaching event. They will test the influence of symbiont type and host gene expression profiles by examining samples of 60 colonies taken at four time points after bleaching. The investigators will also examine the full suite of 280 corals for genetic variation to estimate the relationship between bleaching state, recovery rate and genetic polymorphism. These data will be used to test micro-climate, symbiont, and coral genetics as determinants of bleaching and bleaching recovery. Because the investigators have samples from these 280 colonies before bleaching mortality, this study will provide the first estimate for the evolutionary impact of a bleaching event on coral populations.
attribute	NC_GLOBAL	projects_0_end_date	String	2017-06
attribute	NC_GLOBAL	projects_0_geolocation	String	American Samoa
attribute	NC_GLOBAL	projects_0_name	String	Ecological, evolutionary and physiological responses of corals to a mass bleaching event in American Samoa
attribute	NC_GLOBAL	projects_0_project_nid	String	647914
attribute	NC_GLOBAL	projects_0_start_date	String	2015-07
attribute	NC_GLOBAL	publisher_name	String	Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute	NC_GLOBAL	publisher_type	String	institution
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	summary	String	RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016. This dataset includes accession numbers for 36 RNAseq libraries housed at The National Center for Biotechnology Information (NCBI).
attribute	NC_GLOBAL	title	String	RNA sequence accession numbers for coral colonies that displayed a strong bleaching phenotype at Ofu Island, American Samoa between 2015 and 2016.
attribute	NC_GLOBAL	version	String	2
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	sample		String
attribute	sample	bcodmo_name	String	sample
attribute	sample	description	String	Sample identifier
attribute	sample	long_name	String	Sample
attribute	sample	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	sample	units	String	unitless
variable	colony		String
attribute	colony	bcodmo_name	String	sample
attribute	colony	description	String	Colony identifier
attribute	colony	long_name	String	Colony
attribute	colony	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	colony	units	String	unitless
variable	species		String
attribute	species	bcodmo_name	String	species
attribute	species	description	String	Coral species
attribute	species	long_name	String	Species
attribute	species	units	String	uniless
variable	date		String
attribute	date	bcodmo_name	String	unknown
attribute	date	description	String	Month and year of sampling in format yyyy_mm
attribute	date	long_name	String	Date
attribute	date	units	String	unitless
variable	year		short
attribute	year	_FillValue	short	32767
attribute	year	actual_range	short	2015, 2016
attribute	year	bcodmo_name	String	year
attribute	year	description	String	Year of sampleing
attribute	year	long_name	String	Year
attribute	year	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/
attribute	year	units	String	unitless
variable	month		String
attribute	month	bcodmo_name	String	month
attribute	month	description	String	Month of sampling
attribute	month	long_name	String	Month
attribute	month	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/MNTHXXXX/
attribute	month	units	String	unitless
variable	bleaching_status		byte
attribute	bleaching_status	_FillValue	byte	127
attribute	bleaching_status	actual_range	byte	0, 100
attribute	bleaching_status	bcodmo_name	String	sample_descrip
attribute	bleaching_status	description	String	Bleaching status
attribute	bleaching_status	long_name	String	Bleaching Status
attribute	bleaching_status	units	String	percent
variable	Accession		String
attribute	Accession	bcodmo_name	String	accession number
attribute	Accession	description	String	Genetic accession number at NCBI
attribute	Accession	long_name	String	Accession
attribute	Accession	units	String	unitless
variable	Accession_link		String
attribute	Accession_link	bcodmo_name	String	external_link
attribute	Accession_link	description	String	Link to genetic accession at NCBI
attribute	Accession_link	long_name	String	Accession Link
attribute	Accession_link	units	String	unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.